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The Plant Genome : Just Published


Accepted, edited articles are published here after author proofing to provide rapid publication and better access to the newest research. Articles are compiled into issues at dl.sciencesocieties.org/publications/tpg, which includes the complete archive.

Citation | Articles posted here are considered published and may be cited by the doi.

Joseph, B., J.A. Schlueter, J.Du, M.A. Graham, J. Ma, and R.C. Shoemaker. 2009. Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution. Plant Genome doi:10.3835/plantgenome2009.01.0001

Current issue: Plant Genome 9(3)


    • Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Elisabetta Schilirò, Juan Bautista Barroso, Aureliano Bombarely, Lukas Mueller, Jesús Mercado-Blanco and Francisco Luque
      Transcriptomic Analysis of Olea europaea L. Roots during the Verticillium dahliae Early Infection Process

      Olive cultivation is affected by a wide range of biotic constraints. Verticillium wilt of olive is one of the most devastating diseases affecting this woody crop, inflicting major economic losses in many areas, particularly within the Mediterranean Basin. Little is known about gene-expression changes during plant infection by Verticillium dahliae of woody plants such as olive. A complete RNA-seq transcriptomic analysis of olive tree roots was made. (continued)

      Core Ideas:
      • A transcriptomic RNA-seq analysis was conducted to study the olive–V. dahliae interaction.
      • The transcriptomes of olive roots and V. dahliae were compiled at an early stage of infection.
      • A number of putative genes involved in the plant defense were found.
      • Most of the induced genes in response to the infection are related to protein turnover.
      • An ROS stress-defense response is induced first in the pathogen and later in the plant.

      Published: February 9, 2017

    • Hui Yang, Guixia Shi, Hongyang Du, Hong Wang, Zhenzhen Zhang, Dezhou Hu, Jiao Wang, Fang Huang and Deyue Yu
      Genome-Wide Analysis of Soybean LATERAL ORGAN BOUNDARIES Domain -Containing Genes: A Functional Investigation of GmLBD12

      Plant-specific LBD (LATERAL ORGAN BOUNDARIES Domain) genes play critical roles in various plant growth and development processes. However, the number and characteristics of LBD genes in soybean [Glycine max (L.) Merr.] remain unknown. Here, we identified 90 LBD homologous genes in the soybean genome that phylogenetically clustered into two classes (I and II). The majority of the GmLBD genes were evenly distributed across all 20 soybean chromosomes, and 77 (81.11%) of them were detected in segmental duplicated regions. (continued)

      Core Ideas:
      • Ninety LBD homologous genes were identified in soybean genome.
      • GmLBD genes had wide tissue expression patterns and were regulated by various stresses.
      • GmLBD12 gene was functionally characterized in transgenic Arabidopsis.

      Published: February 9, 2017

    • B.S. Vivek, Girish Kumar Krishna, V. Vengadessan, R. Babu, P.H. Zaidi, Le Quy Kha, S.S. Mandal, P. Grudloyma, S. Takalkar, K. Krothapalli, I.S. Singh, Eureka Teresa M. Ocampo, F. Xingming, J. Burgueño, M. Azrai, R.P. Singh and J. Crossa
      Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize

      More than 80% of the 19 million ha of maize (Zea mays L.) in tropical Asia is rainfed and prone to drought. The breeding methods for improving drought tolerance (DT), including genomic selection (GS), are geared to increase the frequency of favorable alleles. Two biparental populations (CIMMYT-Asia Population 1 [CAP1] and CAP2) were generated by crossing elite Asian-adapted yellow inbreds (CML470 and VL1012767) with an African white drought-tolerant line, CML444. Marker effects of polymorphic single-nucleotide polymorphisms (SNPs) were determined from testcross (TC) performance of F2:3 families under drought and optimal conditions. (continued)

      Core Ideas:
      • Use of GS for improvement to drought tolerance in tropical maize in Asia is relatively new.
      • Positive selection response can be obtained with the use of markers for grain yield under drought.
      • Statistical model used for determining marker effects works in practice and thus stands validated.
      • GEBV-based selection of superior phenotypes (without target stress) leads to rapid genetic gains.

      Published: January 5, 2017

    • Valerio Hoyos-Villegas, Qijian Song and James D. Kelly
      Genome-wide Association Analysis for Drought Tolerance and Associated Traits in Common Bean

      A genome-wide association study explored the genetic basis of variation for drought tolerance and related traits in a Middle American diversity panel comprising 96 common bean (Phaseolus vulgaris L.) genotypes. The panel was grown under irrigated and rainfed conditions and single nucleotide polymorphism (SNP) data were used to explore the genetic diversity and ancestry of the panel. Varying levels of admixtures and distinctly divergent individuals were observed. Estimations of genome-wide heterozygosity revealed that, on average, greater diversity is present in individuals with Mesoamerica (3.8%) ancestry, followed by admixed individuals (2.3%). (continued)

      Core Ideas:
      • GWAS was conducted to identify signals associated with drought tolerance in common bean.
      • Significant signals for drought tolerance were identified.
      • Population structure analysis of a panel of Mesoamerican genotypes revealed heterozygosity.

      Published: December 29, 2016

    • Juan José Ferreira, Ester Murube and Ana Campa
      Introgressed Genomic Regions in a Set of Near-Isogenic Lines of Common Bean Revealed by Genotyping-by-Sequencing

      Genotyping-by-sequencing (GBS) was used to investigate and identify the introgressed genomic regions that corresponded to resistance alleles for anthracnose (Co-2 and Co-3), bean common mosaic virus (BCMV), and bean common mosaic necrosis virus (BCMNV, I and bc-3) in a set of bean near-isogenic lines (NIL). The GBS analysis provided 12,697 single nucleotide polymorphisms (SNPs) although the densities along the chromosomes were not uniform, and some chromosomal regions, such as centromeric or pericentromeric regions, were less tagged. The backcrossing method resulted in the introgression of genomic regions into specific chromosomes. The number of introgressed region-tagging SNPs varied between 1 and 13, representing between 0.33 and 6.88% of the bean genome. (continued)

      Core Ideas:
      • Genotyping-by-sequence allows large-scale genotyping and scanning of chromosomes.
      • Near-isogenic lines are genotypes that are identical except at one or a few loci.
      • Changes detected in NILs are candidate regions that may contain introgressed genes.
      • This is another way to approach the physical position of genes.

      Published: December 22, 2016

    • J. P. Cook, N. K. Blake, H. Y. Heo, J. M. Martin, D. K. Weaver and L. E. Talbert
      Phenotypic and Haplotype Diversity among Tetraploid and Hexaploid Wheat Accessions with Potentially Novel Insect Resistance Genes for Wheat Stem Sawfly

      Genetic diversity in breeding programs can be impaired by fixation of alleles derived from a limited number of founder lines. This is demonstrated with the use of a solid-stem trait derived from the Portuguese landrace ‘S-615’ over 70 yrs ago that is widely used to resist the wheat stem sawfly (Cephus cinctus Norton, WSS) in North America. The objective of this study was to evaluate haplotype diversity underlying the Qss.msub.3BL quantitative trait locus (QTL) that controls the majority of the S-615 derived solid-stem genetic variation using single-nucleotide polymorphism (SNP) assays in a diverse set of 228 solid-stem tetraploid and hexaploid wheat accessions originating from areas of the world infested with various species of WSS. Haplotype analysis showed all WSS-resistant hexaploid wheat varieties in North America, except ‘Conan’, evaluated in this study contain a haplotype associated with the S-615 solid-stem allele. (continued)

      Core Ideas:
      • Haplotype diversity underlying Qss.msub.3BL solid-stem QTL present among solid-stem wheat landraces.
      • Frequency and diversity of haplotypes vary among ploidy levels and geographical regions.
      • New haplotypes potentially containing novel resistance alleles will augment WSS resistance.
      • KASP markers can be used for marker assisted selection of the solid-stem Qss.msub.3BL allele.

      Published: December 22, 2016

    • Yuanwen Guo, Yanqi Wu, Jeff A. Anderson, Justin Q. Moss, Lan Zhu and Jinmin Fu
      SSR Marker Development, Linkage Mapping, and QTL Analysis for Establishment Rate in Common Bermudagrass

      Common bermudagrass has been widely used as a major warm-season turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs). (continued)

      Published: November 29, 2016

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